How can I prevent invisible faces when exporting to FBX file?
This issue is due to the fact that there are N-gons in your model (an N-gon being an N sided polygon). Either FBX doesn't support these or Unity can't import them, but, either way, the solution is to get rid of them. There are many ways to do this, but the fastest is probably to select those faces and Triangulate them (Ctrl + T) and, possibly, convert those to Quads (four sided polygons) (Alt + J).

Another approach, which might get you cleaner results is to use the Bridge Edge Loops tool; this tool doesn't appear to have a shortcut, but you can invoke it either from Edges menu with Ctrl+E > Bridge Edge Loops or by pressing Space (search for operators) and typing it's name. For this tool, you should have two edge loops selected, so delete the N-gon face and select the edges that were there before (Alt + RMB (selection button)) and then execute Bridge Edge Loops.